| MarkerName | Chr | Pos | cytoband | gene.context | Major | Minor | MAF | Effect | StdErr | P.value |
|---|---|---|---|---|---|---|---|---|---|---|
| rs10399947 | 1 | 150,861,960 | 1q21.3 | ARNT–[]–SETDB1 | G | A | 0.369 | -0.06 | 0.01 | 1.02e-08 |
| rs10200279 | 2 | 202,170,655 | 2q33.1 | [ALS2CR12] | C | T | 0.287 | 0.07 | 0.01 | 2.67e-09 |
| rs192481803 | 2 | 35,336,564 | 2p22.3 | [] | C | T | 0.007 | 0.65 | 0.12 | 2.57e-08 |
| rs62246017 | 3 | 71,483,084 | 3p13 | FOXP1—[]—EIF4E3 | G | A | 0.325 | 0.07 | 0.01 | 1.65e-09 |
| rs6791479 | 3 | 189,205,032 | 3q28 | TPRG1—[]—TP63 | A | T | 0.427 | 0.09 | 0.01 | 6.09e-15 |
| rs35407 | 5 | 33,946,571 | 5p13.2 | [SLC45A2] | G | A | 0.042 | -0.47 | 0.04 | 3.89e-31 |
| rs4455710 | 6 | 32,608,858 | 6p21.32 | [HLA-DQA1] | C | T | 0.368 | 0.14 | 0.02 | 5.57e-21 |
| rs12203592 | 6 | 396,321 | 6p25.3 | [IRF4] | C | T | 0.166 | 0.44 | 0.01 | 1.33e-221 |
| rs10944479 | 6 | 90,880,393 | 6q15 | [BACH2] | G | A | 0.189 | -0.09 | 0.02 | 3.75e-09 |
| rs117132860 | 7 | 17,134,708 | 7p21.1 | AGR3—[]—AHR | G | A | 0.021 | 0.25 | 0.04 | 7.97e-09 |
| rs7834300 | 8 | 116,611,632 | 8q23.3 | [TRPS1] | C | G | 0.438 | 0.07 | 0.01 | 2.01e-09 |
| rs1325118 | 9 | 12,619,616 | 9p23 | []–TYRP1 | T | C | 0.304 | -0.07 | 0.01 | 4.38e-08 |
| rs10810657 | 9 | 16,884,586 | 9p22.2 | BNC2–[]—CNTLN | A | T | 0.404 | -0.10 | 0.01 | 1.26e-17 |
| rs57994353 | 9 | 139,356,987 | 9q34.3 | [SEC16A] | T | C | 0.284 | 0.09 | 0.01 | 1.84e-11 |
| rs1126809 | 11 | 89,017,961 | 11q14.3 | [TYR] | G | A | 0.279 | 0.15 | 0.01 | 2.21e-38 |
| rs74899442 | 11 | 115,890,279 | 11q23.3 | CADM1—[]—BUD13 | T | C | 0.004 | 0.60 | 0.11 | 9.09e-08 |
| rs7939541 | 11 | 9,590,389 | 11p15.4 | ZNF143–[]-WEE1 | T | C | 0.410 | 0.08 | 0.01 | 9.23e-12 |
| rs657187 | 12 | 52,898,985 | 12q13.13 | KRT6A–[]-KRT5 | A | G | 0.420 | -0.07 | 0.01 | 1.80e-09 |
| rs721199 | 12 | 96,374,057 | 12q23.1 | [HAL] | C | T | 0.463 | -0.06 | 0.01 | 3.55e-08 |
| rs1800407 | 15 | 28,230,318 | 15q13.1 | [OCA2] | C | T | 0.070 | 0.16 | 0.02 | 2.94e-14 |
| rs1805007 | 16 | 89,986,117 | 16q24.3 | TCF25-[]-TUBB3 | C | T | 0.078 | 0.38 | 0.02 | 1.36e-87 |
| rs6059655 | 20 | 32,665,748 | 20q11.22 | [RALY] | G | A | 0.077 | 0.25 | 0.02 | 1.74e-40 |
| Group | The number of variats |
|---|---|
| Total | 24,707,509 |
| MAF > 1% | 10,792,565 |
| MAF <= 1% | 13,914,944 |
The range of MAF in the original summary stats file was from 0 to 1. Why we have so extremely low MAF? How was MAF computed, using all or a subset of cohorts?
Size values: 500Kb, 1Mb, 2Mb around the lead SNP.
- tables of results: `config`, `snp`, `ncausal`
- locus: 1
-- config:
-- input snps: 2370 fine-mapped + 310 missing Z/LD = 2680 in total
# A tibble: 10 x 4
rank config config_prob config_log10bf
<int> <chr> <dbl> <dbl>
1 1 rs10399947,rs12090215,rs78278355 0.167 23.6
2 2 rs1134067,rs12090215,rs78278355 0.130 23.5
3 3 rs6686064,rs12090215,rs78278355 0.113 23.5
# ... with 7 more rows
-- snp:
# A tibble: 2,680 x 6
snp rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
<chr> <int> <int> <dbl> <dbl> <dbl>
1 rs12090215 19 1 1.00 0.333 13.2
2 rs78278355 1446 2 1.00 0.667 13.2
3 rs10399947 1 3 0.167 0.722 2.50
# ... with 2,677 more rows
-- 9 snps in 95% credible set: rs12090215, rs78278355, rs10399947, rs1134067, rs6686064, rs11204733, rs4970928, rs6660845, rs11587444...
- tables of results: `config`, `snp`, `ncausal`
- locus: 1
-- config:
-- input snps: 4148 fine-mapped + 406 missing Z/LD = 4554 in total
# A tibble: 10 x 4
rank config config_prob config_log10bf
<int> <chr> <dbl> <dbl>
1 1 rs72242061 0.203 3.92
2 2 rs72242061,rs61249550 0.191 7.51
3 3 rs60100018 0.121 3.69
# ... with 7 more rows
-- snp:
# A tibble: 4,554 x 6
snp rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
<chr> <int> <int> <dbl> <dbl> <dbl>
1 rs61249550 3 1 0.475 0.347 3.40
2 rs72242061 1 2 0.395 0.635 3.26
3 rs60100018 2 3 0.184 0.769 2.79
# ... with 4,551 more rows
-- 4 snps in 95% credible set: rs61249550, rs72242061, rs60100018, rs144368575...
- tables of results: `config`, `snp`, `ncausal`
- locus: 1
-- config:
-- input snps: 3278 fine-mapped + 454 missing Z/LD = 3732 in total
# A tibble: 10 x 4
rank config config_prob config_log10bf
<int> <chr> <dbl> <dbl>
1 1 rs16891982,rs35391,rs1363879 0.998 131.
2 2 rs35407,rs35391,rs1363879 0.00238 128.
3 3 rs16891982,rs35391,rs141759051 0.0000403 126.
# ... with 7 more rows
-- snp:
# A tibble: 3,732 x 6
snp rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
<chr> <int> <int> <dbl> <dbl> <dbl>
1 rs35391 9 1 1.00 0.333 13.3
2 rs1363879 75 2 1.00 0.667 7.73
3 rs16891982 1 3 0.998 0.999 5.96
# ... with 3,729 more rows
-- 2 snps in 95% credible set: rs35391, rs1363879...
- tables of results: `config`, `snp`, `ncausal`
- locus: 1
-- config:
-- input snps: 2370 fine-mapped + 310 missing Z/LD = 2680 in total
# A tibble: 10 x 4
rank config config_prob config_log10bf
<int> <chr> <dbl> <dbl>
1 1 rs10399947 0.183 5.54
2 2 rs1134067 0.111 5.32
3 3 rs6686064 0.104 5.29
# ... with 7 more rows
-- snp:
# A tibble: 2,680 x 6
snp rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
<chr> <int> <int> <dbl> <dbl> <dbl>
1 rs10399947 1 1 0.183 0.183 2.73
2 rs1134067 2 2 0.111 0.294 2.47
3 rs6686064 3 3 0.104 0.398 2.44
# ... with 2,677 more rows
-- 9 snps in 95% credible set: rs10399947, rs1134067, rs6686064, rs11587444, rs11204733, rs4970928, rs4970929, rs8444, rs6660845...
- tables of results: `config`, `snp`, `ncausal`
- locus: 1
-- config:
-- input snps: 3278 fine-mapped + 454 missing Z/LD = 3732 in total
# A tibble: 10 x 4
rank config config_prob config_log10bf
<int> <chr> <dbl> <dbl>
1 1 rs16891982 0.999 30.5
2 2 rs35407 0.000982 27.5
3 3 rs28777 0.000000913 24.5
# ... with 7 more rows
-- snp:
# A tibble: 3,732 x 6
snp rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
<chr> <int> <int> <dbl> <dbl> <dbl>
1 rs16891982 1 1 0.999 0.999 6.52
2 rs35407 2 2 0.00100 1.00 0.508
3 rs28777 3 3 0. 1.00 -2.52
# ... with 3,729 more rows
-- 1 snps in 95% credible set: rs16891982...
Size values: 500Kb, 1Mb, 2Mb around the lead SNP.